1 Differential expression analysis using DESeq2

#All sarcomas (ALL)

1.0.1 Samples to compare in the Differential Analysis

1.0.2 Heatmap of the sample-to-sample distances

I applied the dist function to the transpose of the transformed count matrix to get sample-to-sample distances.

There are two groups in the sarcoma PCA which do not cluster according to the sarcoma type, site of disease or HRD score.

1.1 Comparison HRD high and HRD low groups

Summary of differentially expressed genes:

## 
## out of 20001 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)       : 735, 3.7%
## LFC < 0 (down)     : 319, 1.6%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:

## 
## out of 20001 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 479, 2.4%
## LFC < 0 (down)     : 205, 1%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Cutoff values: pvalue = 10e-16 FCcutoff = 1.5

1.1.1 Volcano plot

Genes upregulated in the treated sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side.

1.1.2 Interactive volcano plot

1.1.3 Table of downregulated genes

1.1.4 Table of downregulated genes

1.1.5 Table of upregulated genes

1.2 Heatmap of top 50 DE genes

2 Mixofibrosarcoma (MFS)

2.0.1 Samples to compare in the Differential Analysis

2.1 Comparison treated vs untreated groups

Summary of differentially expressed genes:

## 
## out of 19186 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)       : 28, 0.15%
## LFC < 0 (down)     : 9, 0.047%
## outliers [1]       : 997, 5.2%
## low counts [2]     : 2687, 14%
## (mean count < 19)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:

## 
## out of 19186 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 13, 0.068%
## LFC < 0 (down)     : 5, 0.026%
## outliers [1]       : 997, 5.2%
## low counts [2]     : 693, 3.6%
## (mean count < 6)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Cutoff values: pvalue = 10e-16 FCcutoff = 1.5

2.1.1 Volcano plot

Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side.

2.1.2 Interactive volcano plot

We can observe MAGEC2, MAGEB1, MAGEA3 and PAGE2 upregulated in the HRD high group. However, the number of upregulated genes is very low. ### Counts of most differentially expressed gene

We can observe that MAGEB1, which is one of the most upregulated genes is only up-regulated in three samples. This means that in MFS is difficult to make conclusions based on the RNA seq by comparing HRD high/low groups.

2.1.3 Counts of other Differenatially expressed genes

2.1.4 Table of downregulated genes in Treated samples

## 
## Attaching package: 'shiny'
## The following objects are masked from 'package:DT':
## 
##     dataTableOutput, renderDataTable

2.1.5 Table of upregulated genes in Treated samples

2.2 Heatmap of top 50 DE genes

3 Differential expression analysis using DESeq2

4 Undeddifferentiated Pleomorphic Sarcoma (UPS)

4.0.1 Samples to compare in the Differential Analysis

4.1 Comparison treated vs untreated groups

Summary of differentially expressed genes:

## 
## out of 19201 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)       : 98, 0.51%
## LFC < 0 (down)     : 24, 0.12%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:

## 
## out of 19201 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 60, 0.31%
## LFC < 0 (down)     : 12, 0.062%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Cutoff values: pvalue = 10e-16 FCcutoff = 1.5

4.1.1 Volcano plot

Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side.

4.1.2 Interactive volcano plot

4.1.3 Counts of most differentially expressed gene

4.1.4 Counts of other Differenatially expressed genes

4.1.5 Table of downregulated genes

4.1.6 Table of upregulated genes

4.2 Heatmap of top 50 DE genes

5 Differential expression analysis using DESeq2

6 Leiomyosarcoma (LMS)

6.0.1 Samples to compare in the Differential Analysis

6.1 Comparison treated vs untreated groups

Summary of differentially expressed genes:

## 
## out of 19549 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)       : 141, 0.72%
## LFC < 0 (down)     : 82, 0.42%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:

## 
## out of 19549 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 108, 0.55%
## LFC < 0 (down)     : 58, 0.3%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Cutoff values: pvalue = 10e-16 FCcutoff = 1.5

6.1.1 Volcano plot

Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side.

6.1.2 Interactive volcano plot

6.1.3 Counts of most differentially expressed gene

6.1.4 Counts of other Differenatially expressed genes

6.1.5 Table of downregulated genes

6.1.6 Table of upregulated genes

6.2 Heatmap of top 50 DE genes

7 Differential expression analysis using DESeq2

8 Uterine Leiomyosarcoma (uLMS)

8.0.1 Samples to compare in the Differential Analysis

8.1 Comparison treated vs untreated groups

Summary of differentially expressed genes:

## 
## out of 19122 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)       : 586, 3.1%
## LFC < 0 (down)     : 171, 0.89%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:

## 
## out of 19122 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 369, 1.9%
## LFC < 0 (down)     : 74, 0.39%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Cutoff values: pvalue = 10e-16 FCcutoff = 1.5

8.1.1 Volcano plot

Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side.

8.1.2 Interactive volcano plot

8.1.3 Counts of most differentially expressed gene

8.1.4 Counts of other Differenatially expressed genes

8.1.5 Table of downregulated genes

8.1.6 Table of upregulated genes

8.1.7 Heatmap top 50 differentially expressed genes

9 Differential expression analysis using DESeq2

10 ddLPS

10.0.1 Samples to compare in the Differential Analysis

10.1 Comparison treated vs untreated groups

Summary of differentially expressed genes:

## 
## out of 19594 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)       : 153, 0.78%
## LFC < 0 (down)     : 352, 1.8%
## outliers [1]       : 0, 0%
## low counts [2]     : 0, 0%
## (mean count < 0)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:

## 
## out of 19594 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 89, 0.45%
## LFC < 0 (down)     : 211, 1.1%
## outliers [1]       : 0, 0%
## low counts [2]     : 760, 3.9%
## (mean count < 5)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Cutoff values: pvalue = 10e-16 FCcutoff = 1.5

10.1.1 Volcano plot

Genes upregulated in the HRD high sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side.

10.1.2 Interactive volcano plot

10.1.3 Counts of most differentially expressed gene

10.1.4 Counts of other Differenatially expressed genes

Other genes of interest such as B-Catenin (CTNNB1) abd TP53 are also upregulated in the treated group.

10.1.5 Table of downregulated genes

10.1.6 Table of upregulated genes

10.1.7 Heatmap top 50 differentially expressed genes

11 Differential expression analysis using DESeq2

12 MPNST

12.0.1 Samples to compare in the Differential Analysis

12.1 Comparison treated vs untreated groups

Summary of differentially expressed genes:

## 
## out of 19356 with nonzero total read count
## adjusted p-value < 0.1
## LFC > 0 (up)       : 316, 1.6%
## LFC < 0 (down)     : 135, 0.7%
## outliers [1]       : 858, 4.4%
## low counts [2]     : 1074, 5.5%
## (mean count < 11)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Summary of differentially expressed genes. Adjusting cut-off for and FDR of 0.05:

## 
## out of 19356 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0 (up)       : 176, 0.91%
## LFC < 0 (down)     : 59, 0.3%
## outliers [1]       : 858, 4.4%
## low counts [2]     : 0, 0%
## (mean count < 4)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results

Cutoff values: pvalue = 10e-16 FCcutoff = 1.5

12.1.1 Volcano plot

Genes upregulated in the treated sample are in the right of the volcano plot, whilst downregulated genes are in the left hand side.

12.1.2 Interactive volcano plot

12.1.3 Table of downregulated genes

12.1.4 Table of upregulated genes

12.1.5 Heatmap top 50 differentially expressed genes

Copyright © 2022 Alicia Pliego. FTP lab. All rights reserved.